The mission of the Biomedical Informatics Core is to provide professional expertise in informatics to enable interpretation of results generated by matrix assisted laser desorption-ionization mass spectrometry (MALDI-MS) imaging high throughput technologies to study the biology of breast cancer and the molecular basis of its response to therapy. Protein profiles are important as they are representative of the functional entities that define the phenotype of the cell. Primary objectives for the core include: 1) Implementation of a secure web accessible data warehouse with data retrieval tools that will integrate tissue specific data including tissue bank inventories, clinical information to characterize the tissue donors, and MALDI-MS imaging experimental results; 2) Consultation regarding implementation of methods for MALDI-MS imaging signal processing including spectral alignment, data volume reduction, and correlation with histological images. The Core is available to design novel methods in-house where there is not an existing standard for these operations secondary to the innovative and exploratory nature of the technology; 3 ) Selection of candidates for mechanistic models of action based on a combination of statistical significance of protein signatures and expert knowledge, both internal and from public databases; 4) Establishment of a data laboratory for the translation into practice of new methods of data exploration. The ultimate goal is to integrate expert knowledge, massive data sets, and statistical analysis into a single framework with data mining tools that we can use to derive molecular mechanisms for diagnosis, prognosis, and prediction.